[BioLib-dev] Merging libsequence into main

[Xin Shuai]

Thank you, pjotr, I really learnt a lot about git. Following your
instruction, I've already created a new 'master' branch and it looks just as
the same as my 'master_conflict' branch. Currently I'm still in the process
of updating your libsequence & boost submodule. Later on, I 'll concentrate
on fixing modifying the libsequence files. As you mentioned, I plan to put
my modified file to:
./src/clibs/libsequence/include/.
and leave the /contrib untouched. I think I also have to change the file
including path.
Is that OK?

With regards to the patch, I decided to email them to you.(libsequence-1.6.6
and boost).
You mentioned that I can get the patch by
git commit

Do you mean that I can directly find the patch file in my tree?

I also consult the git manual and learned a command to generate the patch:
$ git format-patch origin

On Sat, Aug 1, 2009 at 4:12 AM, <pjotr.prins14 at thebird.nl> wrote:

> On Fri, Jul 31, 2009 at 12:01:32PM -0400, Xin Shuai wrote:
> > Except for the doubt I raised in my last email(I really don't dare to
> commit
> > freely this time unless you told me nothing is wrong), I've already
> updated
> > the contrib with two submodules: libsequence-1.6.6 and boost.
>
> I would have created another remote branch. That way it would have
> been possible for me to see the differences. Now I am blind to the
> latest changes.
>
> > Regarding to your error, yes, I once met them before. So I modified
> > a few .hpp , .cc and .tcc files to make them work for swig. That's
> > way I once asked you if it is OK for me to modify the original
> > files.
> >
> > I attached a txt file which documents all the files I have modified and
> how.
>
> Ah, that is cool. I see you have fixed a number of problems by
> modifying BOOST and libsequence sources. The only problem is that I
> don't have them in the tree now.
>
> The nice thing is that we actually have both libraries as git
> repositories in biolib(!). This means we can clone the trees onto our
> own github accounts, and push the patches. That way we can make
> visible what works and doesn't work - and share the changes.
>
> If you use my latest libsequence branch and run
>
>  git submodule -i update
>
> you will have both repositories locally. Let's start with a change to
> libsequence:
>
>  cd contrib/libsequence-1.6.6
>  git checkout -b xin    # important since a git submodule is a virtual
> branch
>  # hack hack
>  # test
>  git commit
>
> Now you have patches. So what next? Two options, clone the
> libsequence library at http://github.com/pjotrp/libsequence/tree on
> github and push the patches to your tree.
>
> This is nice. I can pull from that tree.
>
> Another option is to mail me the patches (as generated by git).
>
> The same thing can be done for the BOOST tree. I cloned it from
> git://gitorious.org/boost/svn.git. Unfortunately it is
> large and may not fit into your free github account. You'll have to
> either upgrade github, or I need add you to my github account, or you
> send me patches. What do you prefer?
>
> BTW, fixing upstream libraries - you have to make a call. Really
> changes should go in we can send upstream to the maintainers. Just
> commenting out problematic code is not a 'solution'. For isolated
> cases there are a number of options:
>
>  1. Tell SWIG to ignore the code (renames, macros)
>  2. Create a derived class that is used by SWIG, rather than the
>  parent
>
> If it is unavoidable to parse the master file, and SWIG cracks, maybe
> we can have a copy of that one particular file in the biolib tree,
> which is compiled, rather than the one in contrib. So problematic.h
> is found in:
>
>  ./src/clibs/libsequence/include/problematic.h
>
> rather then
>
>  ./contrib/libsequence/include/problematic.h
>
> In other words, fixing the master repositories should be useful to
> upstream users. Otherwise we need to hack it in biolib itself.
>
> Pj.
>



-- 
Xin Shuai (David)
PhD of Complex System in School of Informatics
Indiana University Bloomington
812-606-8019